An altered intestinal microbiota composition has been associated with IBD. However, it is not clear whether gut dysbiosis contributes to IBD pathogenesis or is a result of intestinal inflammation.

Analysis of dysbiosis in this study. GF, germ-free

Nagao-Kitamoto et al investigated this question by collecting stool samples from 5 patients with Crohn’s disease (CD), 4 patients with ulcerative colitis (UC), and 5 healthy individuals (controls). The authors diluted the samples and administered them orally to germ-free mice. Fecal samples were then collected from the mice and analyzed by 16S ribosomal RNA sequencing, while colon tissues were analyzed for expression of genes and proteins.

Compared with the fecal microbiota of the control donors, the fecal microbiota from UC donors had a lower abundance of Firmicutes, a greater abundance of Proteobacteria, and more variability in the abundances of predominant bacterial taxa among individual samples. There were less obvious differences in the fecal microbes of donors with CD and controls.

After transfer to germ-free mice, the groups still had different community structures, although the between-group differences were not statistically significant. The diversity of the CD and UC donor communities was significantly lower compared with that of the control donors, indicating that the mice colonized with the microbiota from patients with IBD were dysbiotic.

The authors attempted to predict the functions of the microbial communities using the phylogenetic investigation of communities by reconstitution of unobserved states algorithm. They found increases in genes related to flagellar assembly and bacterial motility proteins and reductions in genes involved in certain metabolic pathways, such as carbohydrate and bile acid metabolism, in mice that received microbiota from patients with CD, compared with controls.

Mice that received microbiota from patients with UC had increases in genes that regulate glycolysis and gluconeogenesis, and reductions in genes associated with bacterial homeostasis (DNA replication and peptidoglycan synthesis) and certain metabolic pathways (propanoate metabolism).

The authors propose that the dysbiosis observed in the microbiota from patients with IBD compromises its metabolic function.

When the authors analyzed gene expression profiles in the colonic mucosa of the mice, they found that colonization with the microbiota from controls induced expression of genes associated with the epithelial response to microbes (Reg3b/3g, Cldn4, Duox2, Duoxa2, and Saa3) and immunoglobulin-related genes.

Although colonization of mice with microbiota from patients with CD induced an immune response (based on Th17, Th1, and IL1B signaling), the microbiota sample from only 1 patient induced intestinal pathology in mice.

However, colonization of Il10–/– mice, which are prone to colitis, with microbiota from patients with CD led to intestinal inflammation and severe colitis. The microbiota from the control patients had no effect in these mice.

Nagao-Kitamoto et al observed that levels of flagellin were higher in feces from mice colonized with microbiota from patients with CD than controls. The increase in levels of flagellin in mice receiving the CD microbiota was even higher in the Il10-/- mice. The authors propose that the CD microbiota contains bacteria that have the potential to express flagellin, but flagellin expression is not turned on under physiological conditions.

Colonization with microbiota from patients with UC increased colonic expression of Saa3 and Duoxa2, compared with control microbiota. Genes related to lipid metabolism (Retn, Abcg5/8, Adipoq, Apoc1, Apol7a) and some Th17-related genes (Rorc, Retnla, Ccl20) were expressed at greater levels in colon tissues of mice that received microbiota from patients with UC than CD.

These findings show that altered microbiota from patients with CD or UC seem sufficient to alter the intestinal mucosa in a way that promotes inflammation.

The authors state that although an increased proportion of Proteobacteria was observed in the fecal microbiota of donors with IBD, compared with controls, this difference was not observed in fecal microbiota of mice colonized with microbes from patients with IBD vs controls. They propose that this could be because intestinal inflammation is required for Proteobacteria to bloom in the gut, and recipient mice did not have sufficient inflammation. Likewise, the functional differences detected in donor microbiota samples did not fully correlate those of mice because in 16S rRNA sequencing results.

Nagao-Kitamoto et al add that other features related to diet and environment of mice also affect reconstitution of the microbiota, which is a limit of this model.

In an editorial that accompanies the article, Benoit Chassaing explains that the study benefited from positive-pressure individual ventilated cages (IVCs)—a recent technical advance. Other studies of germ-free animals use isolators, where all the animals are housed inside a single unit and harbor the same microbiota. The IVCs allows multiple conditions to be compared in parallel, and improves the simultaneous analysis of multiple groups. This advance should increase studies of the role of the intestinal microbiota in the development of intestinal inflammation, carcinogenesis, and other disorders associated with an altered microbiome.

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About the Author

Dr. Kristine Novak is the science editor for Gastroenterology and Clinical Gastroenterology and Hepatology. She has worked as an editor at biomedical research journals and as a science writer for 15 years, covering advances in gastroenterology, hepatology, cancer, immunology, biotechnology, molecular genetics, and clinical trials. She has a PhD in cell biology and an interest in all areas of medical research.